I think this is a good idea.

With the quick swap, we're pretending to throw away the partially loaded clip, yes?

You could go the extra mile and have it actually thrown on the ground so you can recover it later if you get the chance.

If I recall correctly, Firearms (an ancient mod for Half-Life 1) did something about the magazine problem you mentioned. Your spare ammo was not listed in bullets, but in magazines. When you reloaded a half-used mag it was kept on your person, and you could use a command later on to merge any half-used mags you were carrying.

Some players, myself included, might think of the quick reload button as the "wrong" way to reload, though. I remember in Metro 2033 there were two kinds of ammo: The cheap ammo did less damage, but good ammo was the currency of the shops and the exchange rate was something like one good shell for three crummy ones. You could switch to better ammo any time, and get more damage per shot, but I never did that, because it felt like a weakness, like I had to turn on easy mode and buy my way through a tough fight. So I'd die and retry a dozen times until I got all headshots with the crappy bullets in order to conserve my "money". It could be that players will be disinclined to use the quick reload, and instead try time and again to manage their fights such that they're always counting rounds and timing reloads to maximize efficiency of inventory.

Adding in the "clean up" method that JoeCooper describes and the mag consolidation system MartyrOfKharak mentioned could help alleviate that problem. Knowing that you can go back and retroactively undo the harm you've done with the faster move would free up my conscience when the fighting's hairy, and I'd be able to take full advantage of the system. On the other hand, it would add some down time and scavenger hunting to the game's pace, since we OCD gamers would have a few minutes of sweeping and combining after each victory.